OETorLib

class OETorLib

Stores and manages torsion libraries used during conformer generation. Torsion rules can be loaded from files or added as SMARTS-based rule strings, and are consulted by OETorDriver when sampling rotatable-bond dihedral angles.

Constructors

OETorLib(const unsigned type = OETorLibType::Default)

Default and copy constructors. The constructor with the type parameter allows the user to set the torsion library type from values in the OETorLibType namespace.

operator=

OETorLib & operator=(const OETorLib &)

Assignment operator.

operator bool

operator bool() const

Returns false if the OETorLib object is empty, otherwise returns true.

AddTorsionLibrary

bool AddTorsionLibrary(const std::string &)
bool AddTorsionLibrary(OEPlatform::oeistream &)

Takes a string or an oeistream object to add a torsion library. This will put the new torsion library above the current torsion library, which means that they will be checked first for a match. To replace the torsion library, call OETorLib::SetTorsionLibrary. The method returns true if the library is added successfully.

AddTorsionRule

bool AddTorsionRule(const std::string &)

Adds a single torsion rule as a string. The format for rules is a SMARTS pattern followed by the torsion angles. The method returns true if the rule is added successfully. The following is an example of a general rule:

[*:1][CH2:2][a:3][a:4] 0 180 90 -90 45 -45 135 -135

The following code demonstrates how to add a new torsion rule to an existing OEOmega object named omega.

Example of adding a new torsion rule

// Adding the torsion rule "[O:1]=[C:2]-[O:3][CH3:4] 90" as a string
// This takes precedent over previous rule
OETorLib torLib;
const char *rule = "[O:1]=[C:2]-[O:3][CH3:4] 90";
if (!torLib.AddTorsionRule(rule))
  OEThrow.Fatal("Failed to add torsion rule: %s", rule);
omegaOpts.SetTorLib(torLib);
omega.SetOptions(omegaOpts);

if(omega(mol))
  OEWriteMolecule(ofs, mol);

See the appendix for a full listing.

The new rule will take precedence over all rules previously added to this object either from a file or from calling this method.

bool AddTorsionRule(OEChem::OEQMolBase &qmol,
                    std::vector<int> &degrees)

The next signature of AddTorsionRule takes a generic OEQMolBase with a corresponding std::vector<int> containing the angles. The pattern represented by OEQMolBase should have map indices set on the atoms considered in the torsion. In SMARTS, this means the atoms should have map indices numbered from 1 to 4. This can theoretically allow torsion rules to be written in other query file formats provided there is a method for setting the appropriate map indices. The following code demonstrates how to initialize an OEQMolBase and use it to define a new torsion rule.

Example of adding a new torsion rule from a query molecule

// Adding torsion rule "[O:1]=[C:2]-[O:3][CH3:4] 45" as a query
// molecule. This takes precedent over default rule
OEQMol qmol;
OEParseSmarts(qmol,"[O:1]=[C:2]-[O:3][CH3:4]");
std::vector<int> degrees;
degrees.push_back(45);

OETorLib torLib;
if (!torLib.AddTorsionRule(qmol, degrees))
  OEThrow.Fatal("Failed to add torsion rule");
omegaOpts.SetTorLib(torLib);
omega.SetOptions(omegaOpts);

if (omega(mol))
  OEWriteMolecule(ofs, mol);

See the appendix for a full listing.

ClearTorsionLibrary

void ClearTorsionLibrary()

Clears the current torsion library. Omega cannot operate with an empty torsion library, so a new torsion library must be set before running Omega.

GetTorRule

const OEChem::OESubSearch* GetTorRule(const OEChem::OEMolBase&,
                                      const OEChem::OEBondBase&) const

Returns the torsion rule associated with the specified bond of the specified molecule. The method returns a null pointer if a torsion rule is not found. The rules are stored as OESubSearch objects.

GetTorRules

OESystem::OEIterBase<OEChem::OESubSearch>* GetTorRules()

Returns an iterator over the torsion rules. The rules are stored as OESubSearch objects.

HasTorRule

bool HasTorRule(const OEChem::OEMolBase&, const OEChem::OEBondBase&) const

Checks if a torsion rule exists with the specified bond of the specified molecule. Returns true if a rule exists.

ResetTorsionLibrary

bool ResetTorsionLibrary()

Resets the torsion library stored internally by Omega. The method returns true if the library is reset successfully.

SetTorsionLibrary

bool SetTorsionLibrary(const std::string &)
bool SetTorsionLibrary(OEPlatform::oeistream &)
bool SetTorsionLibrary(unsigned int type)

Replaces the current torsion library with the one passed in as an argument. If the argument is a type, it is expected to be a value in the OETorLibType namespace. The method returns true if the library is set successfully.